The enable/disable feature is provided by this attribute in each .desktop file:

X-GNOME-Autostart-enabled=true (or false)

If a user toggles enable/disable status of a given application (without deleting it) that was in the system folder, it is copied to the user directory and then the attribute X-GNOME-Autostart-enabled is changed. If a user deletes a given application from the list, the .desktop is copied to user folder with the Hidden=true attribute (or the file is simply deleted if it was present just in the user directory)

Files in both user and system folder does not need to be marked as executable. Default permission is 644 (rw-r--r--). Executable permission for .desktop files are only useful for launchers in your desktop area (the workspace), so they show their icon and allow double-click to start the application. For Dash, Launcher, Autostart and menus in general the executable bit is irrelevant.

KDE used to have its own autostart directories, but nowadays they follow the XDG spec. Maybe ~/.kde/Autostart still works too, but for cross-compability it's better to use the XDG dirs
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MestreLionMay 16 '13 at 11:46